deviations for the S22 benchmark set of noncovalent interactions for 11 std. We have developed a highly parallelized QM/MM implementation in the NAMD and OpenAtom simulation packages, using the dual grid, dual length scale method for combined plane-wave and Euler exponential spline-based QM/MM simulations. Furthermore, ATP binding and/or hydrolysis by NBD2, but not NBD1, is required for MRP1 to shift from a high to low affinity substrate binding state. Its rotation is driven by the free energy obtained from ATP hydrolysis. It is expected that the proton shuttle mechanisms unraveled for hGBP1 apply to many classes of GTPases/ATPases that possess an optimally-arranged hydrogen bonding network, which connects the catalytic water to a proton acceptor. In the simulation of the ATP/apo state, we obsd., for the first time, conformers of the active site with the canonical geometry for an in-line nucleophilic attack on the ATP γ-phosphate. of time-resolved FTIR data revealed two apparent rate consts. through robust numerical criteria. Using time-resolved crystallography, we show that hydrolysis of PPi is an intrinsic and critical step of the DNA synthesis reaction catalyzed by dPols. processes. NIH step (RDS) is proton transfer (PT) from the lytic water mol., which is strongly activated by a metaphosphate generated by a preceding Pγ-Oβ bond dissocn. and cutoff radii that are both computed from first principles. giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3- group based on the structure of a RhoA/GAP-GDP-MgF3- TSA complex. Figure 1. Three-dimensional structures of members of the G protein superfamily are considered in light of other biochem. values, and their combination properly describes both membrane and protein structural properties. The results expose previously unobserved structural intermediates of the NBDs arising from asym. Differences in duty ratio can explain the diversity of structures, speeds and oligomerization states of members of the large kinesin, myosin and dynein families of motors. mechanics (QM/MM) studies of this step have been published, which have substantially contributed to the thinking about the catalytic mechanism. of substrates, indicating that Pdr5 is an uncoupled ABC transporter that constantly hydrolyzes ATP to ensure active substrate transport. structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. m values for ATP and ITP hydrolysis are nearly identical, so these interactions are not likely to play a large role in recognition, with antigen processing (TAP) plays an important role in intracellular peptide transport from the mitochondrial matrix of Saccharomyces cerevisiae. at ∼1°, and reproduces exptl. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated mols. ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiol. The present work clarifies the above point by considering the hydrolysis of phosphate monoesters. We propose a rotation of an O-H bond in the transition between two pentacoordinated structures, during which an overall transition state was identified with an activation energy of 50 kcal/mol. A review. Based on the modified Perdew and Wang exchange functional (MPW) and Becke's 1995 correlation functional (B95), we developed two hybrid meta d. functional theory (HMDFT) methods, namely MPW1B95 and MPWB1K. 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experimental models of phosphate monoester hydrolysis, Resolving Apparent Conflicts between Theoretical and Experimental Models of Phosphate Monoester Hydrolysis, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvVyrtb%252FK&md5=448f7c892b348d7305bac8880beaa703, Phosphate release in F1-ATPase catalytic cycle follows ADP release, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1Slur7L&md5=7d357aa1eba821e7acc939432dbbb704, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXitFKlsL0%253D&md5=fb635fc6c001e3e241f554b585fb2283, ABC transporters: a riddle wrapped in a mystery inside an enigma, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFyqtbvM&md5=f8aab82bd16f235200fbe67e23ce5f51, 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https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXms1Omt7c%253D&md5=f2b0f45f5154bdead4501e6dd9fd77fc, Cooperative, ATPdependent association of the nucleotide binding cassettes during the catalytic cycle of ATP-binding cassette transporters, Cooperative, ATP-dependent association of the nucleotide binding cassettes during the catalytic cycle of ATP-binding cassette transporters, American Society for Biochemistry and Molecular Biology, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XkslyqsLc%253D&md5=25584882fc6b0066d1f8475030224f9e, The conserved glutamate residue adjacent to the Walker-B motif is the catalytic base for ATP hydrolysis in the ATP-binding cassette transporter BmrA, The Conserved Glutamate Residue Adjacent to the Walker-B Motif Is the Catalytic Base for ATP Hydrolysis in the ATP-binding Cassette Transporter BmrA, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXovFKktrk%253D&md5=a853c5db85c57aacb19dce58e960e8fc, Catalytic mechanism of the maltose transporter hydrolyzing ATP, Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXitVSitrfI&md5=d72f6e6d044c1d7ea4688a5609611db3, ATP hydrolysis mechanism in a maltose transporter explored by QM/MM metadynamics simulation, https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1aqtrfE&md5=24065926344695b763da1657785e153c, The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism, The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism, 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